[2024-01-24 12:09:05,477] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:09:05,479] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:09:05,479] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a4e0913-c183-4cef-860d-7ebbe97fb106/dqc_reference
[2024-01-24 12:09:06,706] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:09:06,707] [INFO] Task started: Prodigal
[2024-01-24 12:09:06,708] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb13e4af-ae9a-4146-9871-e97e0cdb73de/GCF_001653565.1_ASM165356v1_genomic.fna.gz | prodigal -d GCF_001653565.1_ASM165356v1_genomic.fna/cds.fna -a GCF_001653565.1_ASM165356v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:09:27,281] [INFO] Task succeeded: Prodigal
[2024-01-24 12:09:27,282] [INFO] Task started: HMMsearch
[2024-01-24 12:09:27,282] [INFO] Running command: hmmsearch --tblout GCF_001653565.1_ASM165356v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a4e0913-c183-4cef-860d-7ebbe97fb106/dqc_reference/reference_markers.hmm GCF_001653565.1_ASM165356v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:09:27,633] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:09:27,634] [INFO] Found 6/6 markers.
[2024-01-24 12:09:27,700] [INFO] Query marker FASTA was written to GCF_001653565.1_ASM165356v1_genomic.fna/markers.fasta
[2024-01-24 12:09:27,700] [INFO] Task started: Blastn
[2024-01-24 12:09:27,700] [INFO] Running command: blastn -query GCF_001653565.1_ASM165356v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a4e0913-c183-4cef-860d-7ebbe97fb106/dqc_reference/reference_markers.fasta -out GCF_001653565.1_ASM165356v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:28,280] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:28,283] [INFO] Selected 10 target genomes.
[2024-01-24 12:09:28,284] [INFO] Target genome list was writen to GCF_001653565.1_ASM165356v1_genomic.fna/target_genomes.txt
[2024-01-24 12:09:28,289] [INFO] Task started: fastANI
[2024-01-24 12:09:28,289] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb13e4af-ae9a-4146-9871-e97e0cdb73de/GCF_001653565.1_ASM165356v1_genomic.fna.gz --refList GCF_001653565.1_ASM165356v1_genomic.fna/target_genomes.txt --output GCF_001653565.1_ASM165356v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:09:44,470] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:44,470] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a4e0913-c183-4cef-860d-7ebbe97fb106/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:09:44,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a4e0913-c183-4cef-860d-7ebbe97fb106/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:09:44,483] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:09:44,483] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:09:44,483] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Paenibacillus oryzisoli	strain=1ZS3-15	GCA_001653565.1	1850517	1850517	type	True	100.0	2719	2724	95	conclusive
Paenibacillus plantarum	strain=LMG 31461	GCA_013141695.1	2654975	2654975	type	True	87.4003	1977	2724	95	below_threshold
Paenibacillus pectinilyticus	strain=KCTC13222	GCA_001700435.1	512399	512399	type	True	82.3603	1225	2724	95	below_threshold
Paenibacillus phytorum	strain=LMG 31458	GCA_013141715.1	2654977	2654977	type	True	80.5462	802	2724	95	below_threshold
Paenibacillus germinis	strain=LMG 31460	GCA_013141785.1	2654979	2654979	type	True	80.5321	809	2724	95	below_threshold
Paenibacillus alginolyticus	strain=DSM 5050	GCA_000422905.1	59839	59839	type	True	80.4949	773	2724	95	below_threshold
Paenibacillus marchantiophytorum	strain=CGMCC 1.15043	GCA_014640555.1	1619310	1619310	type	True	80.3931	780	2724	95	below_threshold
Paenibacillus ferrarius	strain=CY1	GCA_002027705.1	1469647	1469647	type	True	80.0491	807	2724	95	below_threshold
Paenibacillus aceris	strain=DSM 24950	GCA_017874035.1	869555	869555	type	True	79.9655	730	2724	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:09:44,487] [INFO] DFAST Taxonomy check result was written to GCF_001653565.1_ASM165356v1_genomic.fna/tc_result.tsv
[2024-01-24 12:09:44,487] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:09:44,487] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:09:44,488] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a4e0913-c183-4cef-860d-7ebbe97fb106/dqc_reference/checkm_data
[2024-01-24 12:09:44,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:09:44,565] [INFO] Task started: CheckM
[2024-01-24 12:09:44,565] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001653565.1_ASM165356v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001653565.1_ASM165356v1_genomic.fna/checkm_input GCF_001653565.1_ASM165356v1_genomic.fna/checkm_result
[2024-01-24 12:10:46,607] [INFO] Task succeeded: CheckM
[2024-01-24 12:10:46,608] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:10:46,630] [INFO] ===== Completeness check finished =====
[2024-01-24 12:10:46,631] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:10:46,631] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001653565.1_ASM165356v1_genomic.fna/markers.fasta)
[2024-01-24 12:10:46,631] [INFO] Task started: Blastn
[2024-01-24 12:10:46,632] [INFO] Running command: blastn -query GCF_001653565.1_ASM165356v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a4e0913-c183-4cef-860d-7ebbe97fb106/dqc_reference/reference_markers_gtdb.fasta -out GCF_001653565.1_ASM165356v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:10:47,380] [INFO] Task succeeded: Blastn
[2024-01-24 12:10:47,385] [INFO] Selected 5 target genomes.
[2024-01-24 12:10:47,386] [INFO] Target genome list was writen to GCF_001653565.1_ASM165356v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:10:47,395] [INFO] Task started: fastANI
[2024-01-24 12:10:47,395] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb13e4af-ae9a-4146-9871-e97e0cdb73de/GCF_001653565.1_ASM165356v1_genomic.fna.gz --refList GCF_001653565.1_ASM165356v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001653565.1_ASM165356v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:10:58,423] [INFO] Task succeeded: fastANI
[2024-01-24 12:10:58,431] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:10:58,432] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_001653565.1	s__Paenibacillus_E oryzisoli	100.0	2719	2724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013204845.1	s__Paenibacillus_E qinlingensis	87.6852	2051	2724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428105.1	s__Paenibacillus_E sp001428105	87.4361	1761	2724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013141695.1	s__Paenibacillus_E plantarum	87.412	1976	2724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428045.1	s__Paenibacillus_E sp001428045	87.3954	1883	2724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:10:58,433] [INFO] GTDB search result was written to GCF_001653565.1_ASM165356v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:10:58,434] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:10:58,439] [INFO] DFAST_QC result json was written to GCF_001653565.1_ASM165356v1_genomic.fna/dqc_result.json
[2024-01-24 12:10:58,439] [INFO] DFAST_QC completed!
[2024-01-24 12:10:58,439] [INFO] Total running time: 0h1m53s